Silva and De Bruyne are better off in very offensive roles and often play either up high in 4-3-3 or 4-2-3-1. They are not very good defensively. Fernandinho is no world beater. Pep's previous midfielders were much better at ball retention and in general were more talented closer to midfield rather than closer to the front line. Also the backline was much better in distribution.
Thiago, Vidal, Lahm, Martinez, Alonso.
Boateng, Alaba, Lahm, Bernat etc
Xavi, Iniesta, Busquets
Pique, Alves etc
The city team just lacks that ability on the backline and in the centre of the park, which is why we have seen the likes of Kolarov at centreback. At the problem is that the premier league is more competitive than the Bundesliga with 2-3 more title viable teams (Arsenal, Liverpool, Chelsea).
Simply put: Pep's current team isn't effective for his playing style, and lacks the quality of his previous teams. And the step of competition makes it even more difficult. But this is typical EPL problems...buy the expensive attacking midfielder, strikers and most importantly...WINGERS (The EPL has this obsession with offensive wingers, and it is to the detriment of the league), and neglect the centre of the pitch.
When Pep has a team perfect for his style, it is scary dominant, but if he doesn't, the team will have lots of holes. I agree that an Italian coach would do better with the current city side.